Changes in atmospheric CO2 on millennial-to-centennial timescales are key components of past climate variability during the last glacial and deglacial periods (70-10 ka), yet the sources and mechanisms responsible for the CO2 fluctuations remain largely obscure. Here we report the C-13/C-12 ratio of atmospheric CO2 during a key interval of the last glacial period at submillennial resolution, with coeval histories of atmospheric CO2, CH4, and N2O concentrations. The carbon isotope data suggest that the millennial-scale CO2 variability in Marine Isotope Stage 3 is driven largely by changes in the organic carbon cycle, most likely by sequestration of respired carbon in the deep ocean. Centennial-scale CO2 variations, distinguished by carbon isotope signatures, are associated with both abrupt hydrological change in the tropics (e.g., Heinrich events) and rapid increases in Northern Hemisphere temperature (Dansgaard-Oeschger events). These events can be linked to modes of variability during the last deglaciation, thus suggesting that drivers of millennial and centennial CO2 variability during both periods are intimately linked to abrupt climate variability. Plain Language Summary Ice cores provide unique records of variations in atmospheric CO2 prior to the instrumental era. While it is clear that changes in atmospheric CO2 played a significant role in driving past climate change, it is unclear what in turn drove changes in atmospheric CO2. Here we investigate enigmatic changes in atmospheric CO2 levels during an interval of the last glacial period (similar to 50,000 to 35,000 years ago) that are associated with abrupt changes in polar climate. To determine the sources and sinks for atmospheric CO2, we measured the stable isotopes of carbon in CO2 and found that the primary source of carbon to the atmosphere was an organic carbon reservoir. Most likely, this carbon was sourced from a deep ocean reservoir that waxed and waned following changes in either the productivity of the surface ocean or stratification of the deep ocean. We also found that atmospheric CO2 can change on the centennial timescale during abrupt climate transitions in the Northern Hemisphere. This observation adds to a growing body of evidence that abrupt changes in atmospheric CO2 are an important component of past carbon cycle variability.